So is there any way to do this outside of using those splicing tools? we have curated list of splice junctions that have been seen to change in certain conditions, (around 200 junctions), we did match those 200 with hisat2's script output and now just need reads mapping to it will bedtools perform such operation? sorry i really do not understand @Pierre's solutions although i am sure it works primarily due to lack of understanding towards java programming

Out put from your program here can be captured to get the splices reads: A: Filtering out the spliced reads from bam file. ?

will this work just did a bit or more research

To generate read counts, you must run QoRTs [4] on each aligned bam file. QoRTs includes a basic function that calculates a variety of QC metrics along with gene-level and splice-junction-level counts. All these functions can be performed in a single step and a single pass through the input alignment file, greatly simplifying the analysis pipeline. For example, to run QoRTs on the first read-group of replicate SHAM1_RG1 from the example dataset:

java -jar /path/to/jarfile/QoRTs.jar QC \
--stranded \
inputData/bamFiles/SHAM1_RG1.bam \
inputData/annoFiles/anno.gtf.gz \
rawCts/SHAM1_RG1/